Heartwood extracts from Amazonian trees cumaru-ferro (Dipteryx odorata), jatoba (Hymenaea courbaril), and guarita (Astronium lecointei) exhibit antioxidant activities comparable with that of α-tocopherol, a well-known antioxidant. This article reports the characterization of the antioxidant compounds in the extracts of the three heartwoods. Silica gel column chromatography of the cumaru-ferro EtOAc extract yielded (-)-(3 R)-7,2′,3′-trihydroxy-4′-methoxyisoflavan and (+)-(3 R)-8,2′,3′-trihydroxy-7,4′-dimethoxyisoflavan. Silica gel column chromatography followed by preparative high-performance liquid chromatography of the jatoba EtOAc extract yielded (-)-fisetinidol and (+)-trans-taxifolin. Chemical structures were assigned using electron-ionization mass spectrometry, 1H and 13C nuclear magnetic resonance (NMR) spectroscopy including nuclear Overhauser effect spectroscopy (NOESY), as well as optical rotation and circular dichroism. Gas chromatography-mass spectrometry demonstrated that the isolated compounds were predominant in the EtOAc extracts. In the guarita EtOAc extract, catechin and gallic acid were identified by comparing their retention times and mass fragmentation patterns with those of authentic samples. Antioxidant activity determined by the 1,1-diphenyl-2-picrylhydrazyl assay demonstrated that all these compounds had activities comparable with that of α-tocopherol.